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Thermodynamic Stability and Folding Kinetics of the Major G-Quadruplex and Its Loop Isomers Formed in the Nuclease Hypersensitive Element in the Human c-Myc Promoter: Effect of Loops and Flanking Segments on the Stability of Parallel-Stranded Intramolecular G-Quadruplexes
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    Thermodynamic Stability and Folding Kinetics of the Major G-Quadruplex and Its Loop Isomers Formed in the Nuclease Hypersensitive Element in the Human c-Myc Promoter: Effect of Loops and Flanking Segments on the Stability of Parallel-Stranded Intramolecular G-Quadruplexes
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    College of Pharmacy, The University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
    § BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States, Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85721, United States, and Department of Chemistry, The University of Arizona, Tucson, Arizona 85721, United States
    *To whom correspondence should be addressed. Telephone: (520) 626-5969. Fax: (520) 626-6988. E-mail: [email protected]
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    Biochemistry

    Cite this: Biochemistry 2010, 49, 43, 9152–9160
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    https://doi.org/10.1021/bi100946g
    Published September 17, 2010
    Copyright © 2010 American Chemical Society

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    Overexpression of the c-Myc proto-oncogene is associated with a broad spectrum of human cancers. Nuclease hypersensitivity element III1 (NHE III1) of the c-Myc promoter can form transcriptionally active and silenced forms, and the formation of DNA G-quadruplex structures has been shown to be critical for c-Myc transcriptional silencing. The major G-quadruplex formed in c-Myc NHE III1 is a mixture of four loop isomers, which have all been shown to be biologically relevant to c-Myc transcriptional control. In this study, we performed a thorough thermodynamic and kinetic study of the four c-Myc loop isomers in a K+ solution. The four loop isomers all form parallel-stranded G-quadruplexes with short loop lengths. While the parallel-stranded G-quadruplex has been known to favor short loop lengths, our results show that the difference in thermodynamic and kinetic properties of the four loop isomers, and hence between the parallel G-quadruplexes with similar loop lengths, is more significant than previously recognized. At 20 mM K+, the average difference in the Tm values between the most stable loop isomer 14/23 and the least stable loop isomer 11/20 is more than 10 °C. In addition, the capping structures formed by the extended flanking segments are shown to contribute to a stabilization of 2−3 °C in Tm for the c-Myc promoter G-quadruplex. Understanding the intrinsic thermodynamic stability and kinetic properties of the c-Myc G-quadruplex loop isomers can aid in our understanding of their biological roles and drug targeting.

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    ΔG25 values for the c-Myc G-quadruplex loop isomers, hysteresis between CD melting and annealing curves of 11/20 with a temperature gradient of 0.5 °C/min, imino regions of 1D 1H NMR spectra of the completely truncated sequences for the four loop isomers, and hysteresis between CD melting and annealing curves of 11/20 and 11/23 loop isomers with temperature gradients of 2 and 4 °C/min. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Biochemistry

    Cite this: Biochemistry 2010, 49, 43, 9152–9160
    Click to copy citationCitation copied!
    https://doi.org/10.1021/bi100946g
    Published September 17, 2010
    Copyright © 2010 American Chemical Society

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